This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Provided by Brendan MacLean on proteomics software engineering 1. Wrote 3 new 20-40 page tutorials on using Skyline 2. 1 week site visit to Aebersold lab at ETH Zurich with presentation and training in use of Skyline 3. Multi-day site visit at Vanderbilt University, Liebler and Tabb labs with presentation and training in use of Skyline 4. Two presentations at CPTC annual conference in D.C. (one in main hall, one break-out tutorial session) 5. Wrote TechTalk article for US HUPO newsletter on targeted proteomics and Skyline 6. Multi-day site visit at Broad Institute, Carr lab with presentation and training in use of Skyline 7. Answered 140 support requests on Skyline support board (many others through direct email) 8. Regular bimonthly instructional updates over WebEx for Verification Working Group 9. Frequent WebEx sessions with Skyline users to help work through issues 10. Taught undergraduates Alana Killeen and Mimi Fung professional software development for independent study and as interns Provided by Gennifer Merrihew on General Mass Spectrometry Analysis 1. Evvie Vincow (UW Genome Sciences, Pallanck lab) Orbi mass spectrometry, sample prep assistance, data analysis 2. Melody Rynerson (Uw Genome Sciences, Swanson lab) LTQ1 mass spectrometry, sample prep assistance, data analysis 3. Renee George (Uw Genome Sciences, Swanson lab) sample prep assistance 4. Sandra Zimmerman (UW Genome Sciences, Berg lab) LTQ1 mass spectrometry, sample prep assistance, data analysis 5. Jan Aagard (UW Genome Sciences, Swanson lab) data analysis 6. Jennifer Anderson (University of Oregon) LTQ1 and LTQ-FT mass spectrometry, sample prep assistance, data analysis 7. Dana Miller (UW Biochemistry) sample prep assistance 8. Alex Zelter (UW Biochemistry, Davis lab) sample prep assistance, data analysis 9. Marnie Johansson (UW Genome Sciences, Akey lab) sample prep assistance 10. Nicole Liachko (VA Puget Sound Health Care System, Kraemer lab) sample prep assistance 11. Max Boeck (UW Genome Sciences, Waterston lab) sample prep assistance Provided by Jesse Canterbury on General Mass Spectrometry Analysis 1. Scott Shaffer (Med Chem, Goodlett): ion funnel &Velos troubleshooting 2. Young-Ah Goo (Med Chem, Goodlett): triple quad operation/method development 3. Christophe Masselson (Med Chem, Goodlett): SAWN-FAIMS experiments 4. J. Scott Edgar (Med Chem, Goodlett): ion funnel operation 5. Katrina Claw (Swanson lab): mass spec operation 6. Andrew Stergachis (Stamatoyannopoulos lab): mass spec operation 7. Sean McIlwain (Noble): DIA data interpretation 8. Marina Spivak (Noble): HCD data interpretation 9. Alex Zelter (Biochem, Davis): instrument operation, method development Provided by Ed Hsieh on General Mass Spectrometry Analysis 1. Judit Marsillach (UW, Medicinal Chemistry, Furlong lab): Mass spec and HPLC operation, Column preparation, DDA and SRM data analysis. 2. Katrina Claw (UW, Genome Sciences, Swanson lab): Mass spec operation. Experimental design. Data analysis and interpretation. 3. Simon Johnson (UW, Pathology, Rabinovitch and Kaeberlein labs): Mass spec operation. Data analysis and interpretation. 4. Andreas Quandt (Institute of Molecular Systems Biology, Malmstrom lab): Bullseye software setup and analysis. 5. Dao-Fu Dai (UW, Pathology, Rabinovitch lab): Sample preparation, data analysis. 6. Tony Chen (UW, Pathology, Rabinovitch lab): Sample cleanup and preparation. 7. Megan Wargacki (UW, Biochemistry, Davis lab): Sample prepration, DDA data analysis. Provided by Jarrett Egertson on General Mass Spectrometry Analysis 1. Nathan Basisty (UW Pathology): Ion trap operation, QC analysis, Data Independent Acquisition and Data Dependent Acquisition-based method development, data interpretation, Linux 2. Jim Hibbard (UW): Data Independent Acquisition method development, Linux, data interpretation, development of new methods for data post-processing 3. Danielle Swaney (UW Genome Sciences): Database searching for dynamic modification analysis Provided by Michael Bereman on General Mass Spectrometry Analysis 1. Michelle Cilia (USDA): Skyline and cleaning of Vantage, nanoLC operation. 2. Andrew Stergachis (Stamatoyannopulos lab) nanoLC troubleshooting 3. Katrina Claw (Swanson lab): Topograph, Relative quantification 4. Alex Zelter (Davis Lab): Use of Skyline